Variant report

Variant	rs2154032
Chromosome Location	chr6:140053704-140053705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139693236..139695894-chr6:140051578..140054001,3	MCF-7	breast:
2	chr6:140041943..140044127-chr6:140052942..140055529,2	K562	blood:
3	chr6:139695095..139697021-chr6:140050621..140053799,3	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10499213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10499214	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962730	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11963532	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11964275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965819	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12055436	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs12055472	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs12055843	0.88[ASN][1000 genomes]
rs12662206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12664473	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17069206	0.88[JPT][hapmap]
rs17069225	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs1936210	0.90[ASN][1000 genomes]
rs1936214	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2096284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2185923	0.89[ASN][1000 genomes]
rs2327993	0.89[ASN][1000 genomes]
rs4520026	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535566	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4896488	0.81[AMR][1000 genomes]
rs55764205	0.88[ASN][1000 genomes]
rs55966840	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60052799	0.81[AMR][1000 genomes]
rs60350063	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60758082	0.88[ASN][1000 genomes]
rs60870127	0.80[ASN][1000 genomes]
rs6570372	0.90[ASN][1000 genomes]
rs6570373	0.89[ASN][1000 genomes]
rs6570374	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6901783	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs6905478	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911905	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6933318	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6933569	0.81[AMR][1000 genomes]
rs73556090	0.89[ASN][1000 genomes]
rs73558032	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73775693	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7743796	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752001	0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs7752323	0.90[ASN][1000 genomes]
rs7756866	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769567	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7772473	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7774968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776193	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9321752	0.87[ASN][1000 genomes]
rs9373246	0.82[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9373247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9373248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9376452	0.80[GIH][hapmap];0.88[JPT][hapmap]
rs9376457	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9385874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385875	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385876	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9389715	0.90[ASN][1000 genomes]
rs9389717	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9399292	0.88[JPT][hapmap]
rs9403113	0.89[ASN][1000 genomes]
rs9403114	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403116	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv516840	chr6:139960833-140053704	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv464065	chr6:140027836-140085873	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv604766	chr6:140027836-140085873	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2154032	MAP3K5	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140050400-140054000	Weak transcription	Ovary	ovary
2	chr6:140053000-140054600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:140053000-140055000	Enhancers	HMEC	breast
4	chr6:140053200-140054200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:140053200-140054200	Enhancers	Rectal Smooth Muscle	rectum
6	chr6:140053200-140054400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:140053200-140054400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:140053200-140054600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:140053200-140054800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr6:140053200-140055000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:140053200-140055000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:140053200-140055000	Enhancers	HUVEC	blood vessel
13	chr6:140053400-140054000	Enhancers	A549	lung
14	chr6:140053400-140054400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:140053400-140054400	Enhancers	Osteobl	bone
16	chr6:140053400-140054800	Enhancers	NHEK	skin
17	chr6:140053600-140054000	Enhancers	NH-A	brain
18	chr6:140053600-140054200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:140053600-140054400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:140053600-140054400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr6:140053600-140054400	Enhancers	HSMM	muscle
22	chr6:140053600-140054400	Enhancers	NHDF-Ad	bronchial
23	chr6:140053600-140054800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:140053600-140055000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:140053600-140055000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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